Size wise, the MK pickups have the same dimension through out the number of string models, whereas the BH2 pickups have different dimensions in regard to their string numbers.
These are the info from Invalid Link Removed regarding the BH2 pickups replacements:
BTB845SC - 5 String - Can be upgraded to Bartolini-Made MK5CBC, MK5S, MK5C, or MK52J.
BTB846SC - 6 String - Bartolini does not yet offer upgrades for this pickup shape.
BTB740 - 4-String - Bartolini does not yet offer upgrades for this pickup shape.
BTB745, BTB845 - 5 String - Can be upgraded to Bartolini-Made MK5CBC, MK5S, MK5C, or MK52J.
BTB746, BTB846 - 6 String - Bartolini does not yet offer upgrades for this pickup shape.
BTB747 - 7 String - Bartolini does not yet offer upgrades for this pickup shape.
Internally, MK1 consists of split coil pickup in reverse P configuration... whereas I suspect the BH2 to be full blade dual coil (haven't owned one with the BH2, so couldn't make sure of it, but I own couple basses with BH1 pickups which are full blade dual coil pickups)... and I'm pretty sure their voicing are different.
And so far, BH pickups are proprietary to Ibanez, as they were being developed by Bill Bartolini together with Ibanez's top engineers, whereas the MK1 are being used by Ibanez as well as other brands such as Lakland and Cort.